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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ), 'gf_id' => 'HOM05D001278', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001278' ), 'data_identifier' => 'HOM05D001278', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001278', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p00860' => 'bna', 'A03p53550' => 'bna', 'A07p26490' => 'bna', 'A07p45440' => 'bna', 'A08p26270' => 'bna', 'A09p38520' => 'bna', 'A10p25000' => 'bna', 'A10p26550' => 'bna', 'Aa31LG3G16000' => 'aar', 'Aa31LG4G330' => 'aar', 'Aa31LG4G340' => 'aar', 'Aa31LG6G4560' => 'aar', 'Aa31LG7G10180' => 'aar', 'Aa31LG9G10170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.589' => 'aag', 'Actinidia01739' => 'ach', 'Actinidia02110' => 'ach', 'Actinidia05193' => 'ach', 'Actinidia10190' => 'ach', 'Actinidia13226' => 'ach', 'Actinidia14444' => 'ach', 'Actinidia22334' => 'ach', 'Actinidia22687' => 'ach', 'Actinidia27459' => 'ach', 'Ah.02g116880' => 'amhyb', 'Ah.05g167120' => 'amhyb', 'Ah.10g035770' => 'amhyb', 'Ah.12g056560' => 'amhyb', 'Ah.16g104520' => 'amhyb', 'AL1G40870' => 'aly', 'AL2G41490' => 'aly', 'AL6G21780' => 'aly', 'AL7G31020' => 'aly', 'Aqoxy6G02692' => 'aox', 'Aqoxy7G00732' => 'aox', 'Aqoxy7G03642' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0TH4I1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.39URSV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BV8AZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D0VJ3P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ELEK5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F09ESD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HI697U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JI0RX7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRS6HW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N79BSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RMWJ30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW7KBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9TVYB' => 'arhy', 'AT1G27450' => 'ath', 'AT1G80050' => 'ath', 'AT4G12440' => 'ath', 'AT4G22570' => 'ath', 'AT5G11160' => 'ath', 'ATR0019G009' => 'atr', 'ATR1153G053' => 'atr', 'Atru.chr13.817' => 'acertr', 'Atru.chr7.2444' => 'acertr', 'Atru.chr9.1364' => 'acertr', 'AUR62007486' => 'cqu', 'AUR62012411' => 'cqu', 'AUR62031533' => 'cqu', 'AUR62037435' => 'cqu', 'AUR62038796' => 'cqu', 'AUR62038797' => 'cqu', 'AUR62039942' => 'cqu', 'BcaB02g07297' => 'bca', 'BcaB03g11735' => 'bca', 'BcaB08g37084' => 'bca', 'BcaC01g00786' => 'bca', 'BcaC01g01611' => 'bca', 'BcaC01g06950' => 'bca', 'BcaC03g13353' => 'bca', 'BcaC04g19255' => 'bca', 'BcaC05g26564' => 'bca', 'BcaC05g26748' => 'bca', 'BcaC08g45288' => 'bca', 'BcaC08g47568' => 'bca', 'BcaNung01690' => 'bca', 'BcaNung01914' => 'bca', 'BcaNung01916' => 'bca', 'BcaNung02493' => 'bca', 'BolC2t06446H' => 'bol', 'BolC3t19671H' => 'bol', 'BolC3t20709H' => 'bol', 'BolC5t31332H' => 'bol', 'BolC6t38057H' => 'bol', 'BolC6t40440H' => 'bol', 'BolC7t45688H' => 'bol', 'BolC9t59393H' => 'bol', 'BraA02t05069Z' => 'bra', 'BraA03t14421Z' => 'bra', 'BraA07t30292Z' => 'bra', 'BraA07t32048Z' => 'bra', 'BraA08t34578Z' => 'bra', 'BraA09t39358Z' => 'bra', 'BraA10t44712Z' => 'bra', 'C02p04880' => 'bna', 'C03p73790' => 'bna', 'C03p84270' => 'bna', 'C05p26180' => 'bna', 'C06p28900' => 'bna', 'C06p54270' => 'bna', 'C07p51890' => 'bna', 'C09p65700' => 'bna', 'CAN.G1217.11' => 'can', 'CAN.G724.10' => 'can', 'CANSAT21G0996' => 'cansat', 'CANSAT25G1599' => 'cansat', 'CANSAT25G1767' => 'cansat', 'CARHR027050' => 'chi', 'CARHR202140' => 'chi', 'CARHR229460' => 'chi', 'CARHR253760' => 'chi', 'Carub.0001s2600' => 'cru', 'Carub.0002s2747' => 'cru', 'Carub.0006s0964' => 'cru', 'Carub.0006s3160' => 'cru', 'Carub.0007s1874' => 'cru', 'Ca_06704_v3' => 'car', 'Ca_15745_v3' => 'car', 'Ca_15908_v3' => 'car', 'Ca_25936_v3' => 'car', 'CBR_g34312' => 'cbr', 'Cc04_g04460' => 'ccan', 'Cc08_g00490' => 'ccan', 'Cc08_g12840' => 'ccan', 'Cc10_g05670' => 'ccan', 'CDE04G0562' => 'cde', 'CDE04G1066' => 'cde', 'CDE07G2031' => 'cde', 'CDE12G0540' => 'cde', 'CDE12G0655' => 'cde', 'Cfa013132' => 'cfa', 'Cfa013679' => 'cfa', 'Cfa023679' => 'cfa', 'Ciclev10002024m.g' => 'ccl', 'Ciclev10002564m.g' => 'ccl', 'Ciclev10009485m.g' => 'ccl', 'Ciclev10022476m.g' => 'ccl', 'CiPaw.07G176100' => 'cil', 'CiPaw.07G224200' => 'cil', 'CiPaw.08G049500' => 'cil', 'CiPaw.11G151400' => 'cil', 'CiPaw.12G107600' => 'cil', 'ClCG00G003020' => 'cla', 'ClCG00G003350' => 'cla', 'ClCG01G003890' => 'cla', 'ClCG08G013440' => 'cla', 'ClCG08G016410' => 'cla', 'ClCG10G002940' => 'cla', 'COL.COLO4_11932' => 'col', 'COL.COLO4_18871' => 'col', 'COL.COLO4_28518' => 'col', 'COL.COLO4_37201' => 'col', 'Cpa.g.sc217.11' => 'cpa', 'Cpa.g.sc217.12' => 'cpa', 'Cpa.g.sc249.6' => 'cpa', 'Cpa.g.sc29.134' => 'cpa', 'Cre17.g704850' => 'cre', 'CsaV3_2G026200' => 'csa', 'CsaV3_2G032170' => 'csa', 'CsaV3_3G002990' => 'csa', 'CsaV3_5G004020' => 'csa', 'CSS0003599' => 'camsi', 'CSS0029609' => 'camsi', 'CSS0036522' => 'camsi', 'CSS0038815' => 'camsi', 'CSS0039340' => 'camsi', 'CSS0043345' => 'camsi', 'CSS0043886' => 'camsi', 'DCAR_001534' => 'dca', 'DCAR_004929' => 'dca', 'DCAR_020075' => 'dca', 'DCAR_025517' => 'dca', 'DCAR_027793' => 'dca', 'Dinv08631' => 'din', 'Dinv21609' => 'din', 'Dinv30613' => 'din', 'Dinv39114' => 'din', 'Dinv39232' => 'din', 'Dinv44966' => 'din', 'Duzib041G0408' => 'dzi', 'Duzib068G0177' => 'dzi', 'Duzib093G1890' => 'dzi', 'Duzib160G0251' => 'dzi', 'Duzib168G2389' => 'dzi', 'Duzib187G0619' => 'dzi', 'Duzib205G1827' => 'dzi', 'Duzib235G0257' => 'dzi', 'ECA232G4372' => 'eca', 'ECA232G4559' => 'eca', 'ECA233G4971' => 'eca', 'ECA247G3697' => 'eca', 'EL10Ac2g04200' => 'bvu', 'EL10Ac5g13020' => 'bvu', 'Eucgr.C02760' => 'egr', 'Eucgr.D02033' => 'egr', 'Eucgr.E00451' => 'egr', 'Eucgr.F02260' => 'egr', 'Eucgr.F03882' => 'egr', 'FAN04G2078' => 'fan', 'FAN08G1306' => 'fan', 'FAN13G0426' => 'fan', 'FAN15G0615' => 'fan', 'FAN15G1021' => 'fan', 'FAN15G2463' => 'fan', 'FAN18G3502' => 'fan', 'FAN20G1813' => 'fan', 'FAN20G3073' => 'fan', 'FAN24G1914' => 'fan', 'FAN24G2735' => 'fan', 'FAN27G0605' => 'fan', 'FAN27G1643' => 'fan', 'FvH4_2g28940' => 'fve', 'FvH4_2g33240' => 'fve', 'FvH4_5g00190' => 'fve', 'Glyma.01G210800' => 'gma', 'Glyma.04G045000' => 'gma', 'Glyma.04G065800' => 'gma', 'Glyma.05G056500' => 'gma', 'Glyma.06G045500' => 'gma', 'Glyma.06G067200' => 'gma', 'Glyma.09G127800' => 'gma', 'Glyma.11G031200' => 'gma', 'Glyma.14G115700' => 'gma', 'Glyma.17G138800' => 'gma', 'Glyma.17G191766' => 'gma', 'Glyma.17G212100' => 'gma', 'Gohir.A05G055600' => 'ghi', 'Gohir.A05G122600' => 'ghi', 'Gohir.A05G209100' => 'ghi', 'Gohir.A06G023700' => 'ghi', 'Gohir.A06G098600' => 'ghi', 'Gohir.A12G219100' => 'ghi', 'Gohir.D05G057700' => 'ghi', 'Gohir.D05G123500' => 'ghi', 'Gohir.D05G212300' => 'ghi', 'Gohir.D06G020800' => 'ghi', 'Gohir.D06G100700' => 'ghi', 'Gohir.D12G221400' => 'ghi', 'Gorai.008G237200' => 'gra', 'Gorai.009G058800' => 'gra', 'Gorai.009G127400' => 'gra', 'Gorai.009G219000' => 'gra', 'Gorai.010G025300' => 'gra', 'Gorai.010G115800' => 'gra', 'GSVIVG01005518001' => 'vvi', 'GSVIVG01009358001' => 'vvi', 'GSVIVG01017349001' => 'vvi', 'GSVIVG01035872001' => 'vvi', 'HanXRQChr02g0046931' => 'han', 'HanXRQChr02g0049451' => 'han', 'HanXRQChr02g0049461' => 'han', 'HanXRQChr02g0058591' => 'han', 'HanXRQChr03g0075481' => 'han', 'HanXRQChr09g0266631' => 'han', 'HanXRQChr11g0327891' => 'han', 'HanXRQChr16g0500311' => 'han', 'HanXRQChr17g0550751' => 'han', 'Haze_21502' => 'cav', 'Haze_22321' => 'cav', 'Hma1.2p1_0210F.1_g089540' => 'hma', 'Hma1.2p1_0242F.1_g100640' => 'hma', 'Hma1.2p1_0243F.1_g100930' => 'hma', 'Hma1.2p1_0753F.1_g212870' => 'hma', 'Hma1.2p1_0819F.1_g223790' => 'hma', 'HPP92_010827' => 'vpl', 'HPP92_015028' => 'vpl', 'HPP92_018750' => 'vpl', 'HPP92_019614' => 'vpl', 'HPP92_021043' => 'vpl', 'HPP92_027421' => 'vpl', 'Hund04505' => 'sun', 'Hund05310' => 'sun', 'Hund11584' => 'sun', 'Hund14595' => 'sun', 'Lalb_Chr05g0214521' => 'lal', 'Lalb_Chr08g0244161' => 'lal', 'Lalb_Chr08g0245521' => 'lal', 'Lalb_Chr11g0062851' => 'lal', 'Lalb_Chr23g0268471' => 'lal', 'Lj1g0015953' => 'lja', 'Lj1g0020719' => 'lja', 'Lj2A212G44' => 'lonja', 'Lj2g0010786' => 'lja', 'Lj4A70T33' => 'lonja', 'Lj4C70G1' => 'lonja', 'Lj5A73G69' => 'lonja', 'Lj8A705T44' => 'lonja', 'Lj8C258G9' => 'lonja', 'Lsat_1_v5_gn_1_24200' => 'lsa', 'Lsat_1_v5_gn_3_1861' => 'lsa', 'Lsat_1_v5_gn_4_131120' => 'lsa', 'Lsat_1_v5_gn_4_87701' => 'lsa', 'Lsat_1_v5_gn_6_2580' => 'lsa', 'Manes.01G077400' => 'mes', 'Manes.02G036700' => 'mes', 'Manes.03G013600' => 'mes', 'Manes.04G112000' => 'mes', 'Manes.05G181000' => 'mes', 'Manes.11G057500' => 'mes', 'Manes.16G123000' => 'mes', 'Manes.18G045401' => 'mes', 'Mapoly0100s0027' => 'mpo', 'MBI04_g32489_MAGBIO' => 'mbi', 'MBI04_g37593_MAGBIO' => 'mbi', 'MBI16_g18629_MAGBIO' => 'mbi', 'MCO02G140' => 'mco', 'MD04G1085600' => 'mdo', 'MD06G1062600' => 'mdo', 'MD08G1086300' => 'mdo', 'MD08G1086400' => 'mdo', 'MD08G1155300' => 'mdo', 'MD15G1071300' => 'mdo', 'MD15G1126400' => 'mdo', 'Medtr3g103010' => 'mtr', 'Medtr3g106780' => 'mtr', 'Medtr4g101460' => 'mtr', 'Medtr5g012210' => 'mtr', 'MELO3C005556.2' => 'cme', 'MELO3C010812.2' => 'cme', 'MELO3C011270.2' => 'cme', 'MELO3C013962.2' => 'cme', 'Migut.A00813' => 'egut', 'Migut.E01806' => 'egut', 'Migut.I00756' => 'egut', 'Migut.N02773' => 'egut', 'MSTRG.11146' => 'ama', 'MSTRG.1939' => 'ama', 'MSTRG.22225' => 'ama', 'MSTRG.22751' => 'ama', 'MSTRG.24370' => 'ama', 'MSTRG.4704' => 'ama', 'Nitab4.5_0000164g0190' => 'nta', 'Nitab4.5_0000312g0400' => 'nta', 'Nitab4.5_0002042g0060' => 'nta', 'Nitab4.5_0002408g0030' => 'nta', 'Nitab4.5_0004319g0010' => 'nta', 'Nitab4.5_0004319g0020' => 'nta', 'Nitab4.5_0009716g0030' => 'nta', 'Nitab4.5_0012315g0010' => 'nta', 'Nn1g01071' => 'nnu', 'Nn1g06152' => 'nnu', 'Nn2g12104' => 'nnu', 'Nn5g30555' => 'nnu', 'Nn6g34024' => 'nnu', 'Nn8g39526' => 'nnu', 'Oeu022283.1' => 'oeu', 'Oeu026499.3' => 'oeu', 'Oeu027842.3' => 'oeu', 'Oeu029334.1' => 'oeu', 'Oeu050874.1' => 'oeu', 'Oeu060115.1' => 'oeu', 'Os02g0613900' => 'osa', 'Os04g0504000' => 'osa', 'Os07g0484800' => 'osa', 'Os12g0589100' => 'osa', 'Os12g0592400' => 'osa', 'Peaxi162Scf00002g00912' => 'pax', 'Peaxi162Scf00081g01515' => 'pax', 'Peaxi162Scf01131g00012' => 'pax', 'PGR031G2407' => 'pgr', 'PGR042G0130' => 'pgr', 'PGR044G1358' => 'pgr', 'PGR083G0920' => 'pgr', 'PGR102G0877' => 'pgr', 'PGSC0003DMG400004744' => 'stu', 'PGSC0003DMG400008007' => 'stu', 'PGSC0003DMG400021527' => 'stu', 'Phvul.001G050500' => 'pvu', 'Phvul.002G061600' => 'pvu', 'Phvul.009G070900' => 'pvu', 'Phvul.009G092200' => 'pvu', 'Potri.001G121400' => 'ptr', 'Potri.006G255900' => 'ptr', 'Potri.014G017200' => 'ptr', 'Potri.018G026200' => 'ptr', 'Pp3c4_7810' => 'ppa', 'Pp3c8_16590' => 'ppa', 'PRCOL_00001594' => 'pco', 'Prupe.1G424200' => 'ppe', 'Prupe.1G482300' => 'ppe', 'Prupe.5G074000' => 'ppe', 'Psat0s3943g0080' => 'psa', 'Psat0ss8367g0320' => 'psa', 'Psat5g029280' => 'psa', 'PSO017G0099' => 'pso', 'PSO017G5832' => 'pso', 'PSO063G1269' => 'pso', 'PSO170G4026' => 'pso', 'PSO170G4734' => 'pso', 'PSO170G6535' => 'pso', 'PSO782G4207' => 'pso', 'QL02p021414' => 'qlo', 'QL12p013087' => 'qlo', 'QL12p037853' => 'qlo', 'RcHm_v2.0_Chr6g0297761' => 'rch', 'RcHm_v2.0_Chr6g0309401' => 'rch', 'RcHm_v2.0_Chr7g0202681' => 'rch', 'Rhsim02G0202300' => 'rsi', 'Rhsim06G0061600' => 'rsi', 'Rhsim07G0105600' => 'rsi', 'Rhsim08G0212400' => 'rsi', 'Sabra01G0093600' => 'sbr', 'Sabra06G0200200' => 'sbr', 'Sabra14G0011000' => 'sbr', 'Sabra18G0028600' => 'sbr', 'SalBow2G1644' => 'sbo', 'SalBow6G0326' => 'sbo', 'SalBow6G1552' => 'sbo', 'SalBow6G3542' => 'sbo', 'Sc01g0009370' => 'sci', 'Sc09g0008170' => 'sci', 'Sc22g0000750' => 'sci', 'Sc26g0004160' => 'sci', 'Sed0001249' => 'sed', 'Sed0003302' => 'sed', 'Sed0004113' => 'sed', 'Sed0013493' => 'sed', 'Sed0020061' => 'sed', 'Sed0024439' => 'sed', 'SEGI_03623' => 'sgi', 'SEGI_18090' => 'sgi', 'SEGI_35216' => 'sgi', 'SEGI_35336' => 'sgi', 'SGA_v2.0_scaffold120G32856' => 'sas', 'SGA_v2.0_scaffold28G11824' => 'sas', 'SGA_v2.0_scaffold37G14758' => 'sas', 'SGA_v2.0_scaffold5G02705' => 'sas', 'SHI20262' => 'shi', 'SMO356G0564' => 'smo', 'Solyc04g077970.4' => 'sly', 'Solyc08g079020.3' => 'sly', 'Sopen04g031560' => 'spe', 'Sopen08g027480' => 'spe', 'Sp1g23690' => 'spa', 'Sp5g35820' => 'spa', 'Sp7g20610' => 'spa', 'TAR375G0294' => 'tar', 'TAR381G0266' => 'tar', 'TAR381G0718' => 'tar', 'TAR625G0899' => 'tar', 'TAR625G0995' => 'tar', 'TAR629G1727' => 'tar', 'TAR636G3253' => 'tar', 'THA.LOC104799234' => 'tha', 'THA.LOC104800442' => 'tha', 'THA.LOC104808414' => 'tha', 'THA.LOC104809810' => 'tha', 'THA.LOC104813702' => 'tha', 'THA.LOC104815023' => 'tha', 'THA.LOC104818612' => 'tha', 'THA.LOC104825773' => 'tha', 'Thecc.03G255800' => 'tca', 'Thecc.06G028900' => 'tca', 'Thecc.08G090200' => 'tca', 'Thecc.09G023200' => 'tca', 'Thhalv10008627m.g' => 'esa', 'Thhalv10014752m.g' => 'esa', 'Thhalv10019519m.g' => 'esa', 'Thhalv10026345m.g' => 'esa', 'TPR.G25928' => 'tpr', 'TPR.G3112' => 'tpr', 'TPR.G33680' => 'tpr', 'TPR.G37614' => 'tpr', 'TWI12G0859' => 'twi', 'TWI12G1476' => 'twi', 'TWI32G1160' => 'twi', 'TWI34G0301' => 'twi', 'TWI56G1486' => 'twi', 'TWI60G1127' => 'twi', 'TWI81G0477' => 'twi', 'unitig_578.g16145' => 'ugi', 'unitig_578.g16562' => 'ugi', 'vmacro11181' => 'vma', 'vmacro14097' => 'vma', 'vmacro19004' => 'vma', 'vmacro21438' => 'vma', 'VMungo0251G3658' => 'vmu', 'VMungo0647G1927' => 'vmu', 'VMungo1215G0969' => 'vmu', 'VMungo1309G2909' => 'vmu', 'VMungo1309G2927' => 'vmu', 'Zm00001eb023390' => 'zma', 'Zm00001eb030440' => 'zma', 'Zm00001eb078070' => 'zma', 'Zm00001eb135050' => 'zma', 'Zm00001eb184610' => 'zma', 'Zm00001eb247050' => 'zma', 'Zm00001eb309120' => 'zma', 'Zm00001eb355910' => 'zma' ) $gf_id = 'HOM05D001278' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001278' ) $data_identifier = 'HOM05D001278' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 8, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355910' $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